Hybrid QM/MM study of thio effects in transphosphorylation reactions

Results of a series of hybrid quantum mechanical/molecular mechanical (QM/MM) activated dynamics simulations of thio effects in the transphosphorylation (methanolysis) of a 2'-ribose, 5'-methyl phosphate-diester under basic conditions are presented. Single and double substitutions in the nonbridging oxygen positions exhibit thio effects in accord with experimental data and show the existence of a stable intermediate. Thio substitution at the 2' and 5' positions resulted in reactions having a single transition state with increased and decreased free energy barriers, respectively, relative to the unsubstituted reaction. In all of the reactions except for the 5' substitution, the rate-limiting step corresponds to exocyclic cleavage. In the 5' substitution reaction, the rate-limiting step corresponds to endocyclic cleavage and shows a considerable reverse thio effect, in accord with experimental observations of phosphates with enhanced leaving groups. Thio substitution at the 3' position results in a mild reverse thio effect that arises from electronic stabilization of the dianionic transition state. The results presented here provide an important step toward the development and application of new hybrid QM/MM methods that, combined with experiment, may provide a detailed picture of the molecular mechanisms of RNA catalysis.     

Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification

Density functional calculations of thio effects on the in-line mechanism of methanolysis of ethylene phosphate (a reverse reaction model for RNA phosphate transesterification) are presented. A total of 12 reaction mechanisms are examined using the B3LYP functional with large basis sets, and the effects of solvation were treated using the PCM, CPCM, and SM5 solvation models. Single thio substitutions at all of the distinct phosphoryl oxygen positions (2', 3', 5', pro-R) and a double thio substitution at the nonbridging (pro-R/pro-S) positions were considered. Profiles for each reaction were calculated in the dianionic and monoanionic/monoprotic states, corresponding to reaction models under alkaline and nonalkaline conditions, respectively. These models provide insight into the mechanisms of RNA transesterification thio effects and serve as a set of high-level quantum data that can be used in the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations and linear-scaling electronic structure calculations.     

Proton transfer in nanoconfined polar solvents. 1. Free energies and solute position

The reaction free energy curves for a model phenol-amine proton-transfer system in a confined CH3Cl solvent have been calculated by Monte Carlo simulations. The free energy curves, as a function of a collective solvent coordinate, have been obtained for several fixed reaction complex radial positions (based on the center-of-mass). A smooth, hydrophobic spherical cavity was used to confine the solvent, and radii of 10 and 15 A have been considered. Quantum effects associated with the transferring proton have been included by adding the proton zero-point energy to the classical free energy. The results indicate the reaction complex position can be an important component of the reaction coordinate for proton-transfer reactions in nanoconfined solvents.     

Effects of thioamide substitutions on the conformation and stability of alpha- and 3(10)-helices

Thiopeptides, formed by replacing the amide oxygen atom with a sp(2) sulfur atom, are useful in protein engineering and drug design because they confer resistance to enzymatic degradation and are predicted to be more rigid. This report describes our free molecular dynamics simulations with explicit water and free energy calculations on the effects of thio substitutions on the conformation of alpha-helices, 3(10)-helices, and their relative stability. The most prominent structural effect of thio substitution is the increase in the hydrogen bond distance from 2.1 A for normal peptides to 2.7 A for thiopeptides. To accommodate for the longer C[double bond]S...H-N hydrogen bond, the (phi, psi) dihedral angles of the alpha-helix changed from (-66 degrees, -42 degrees) to (-68 degrees, -38 degrees), and the rise per turn increased from 5.5 to 6.3 A. For 3(10)-helices, the (phi, psi) dihedral angles (-60 degrees, -20 degrees) and rise per turn (6.0 A) changed to (-66 degrees, -12 degrees) and 6.8 A, respectively. In terms of relative stability, the most prominent change upon thio substitution is the decrease in the free energy difference, Delta A(alpha --> 3(10)), from 14 to 3.5 kcal/mol. Therefore, normal peptides are less likely to form 3(10)-helix than are thiopeptides. Component analysis of the Delta A(alpha --> 3(10)) reviews that the entropy advantage of the 3(10)-helix for both Ac-Ala(10)-NHMe and Act-Alat(10)-NHMe is attributed to the 3(10)-helix being more flexible than the alpha-helix. Interestingly, upon thio substitution, this differential flexibility is even more apparent because the alpha-helix conformation of Act-Alat(10)-NHMe becomes more rigid due to the bulkier sulfur atom.     

Theoretical study of the thermal unimolecular rearrangement of fluoroethylidenes

The thermal unimolecular isomerization of fluoroethylidenes to the corresponding fluoroethylenes has been studied by the MNDO method. It has been shown that fluorine substitution on the carbene carbon increases the activation energy in comparison with the ethylidene rearrangement. To understand the reason for this increase in the activation energy, the charge-transfer effects have been analyzed. Fluorine substitution at other positions does not significantly affect the activation energies. The thermodynamic parameters for the reaction have been evaluated, using vibrational and rotational spectral data calculated in this work. RRKM calculations have been performed and high-pressure Arrhenius parameters calculated. Hydrogen–deuterium kinetic isotope effects indicate that the reaction rates are altered considerably on isotopic substitution, and the change in reaction rates depends upon the position of deuterium substitution, as well as on the number of hydrogens replaced by deuterium atoms. © 1992 John Wiley & Sons, Inc.     

The atmospheric pressure Meerwein reaction

We have already shown that the in-vacuum gas-phase Meerwein reaction of (thio)acylium ions is general in nature and useful for class-selective screening of cyclic (thio)epoxides. Herein we report that this gas-phase reaction can also be performed efficiently at atmospheric pressure under both electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) conditions. This alternative expands the range of molecules that can be reacted by gas-phase Meerwein reaction. Phenyl epoxide, thiirane, 3-methoxy-2,2-dimethyloxirane, propylene oxide, 2,2'-bioxirane, trans-1,3-diphenyl-2,3-epoxypropan-1-one, epichloridrine and propylene oxide are shown to react efficiently in both ESI and APCI conditions. Tetramethylurea (TMU) and (thio)TMU were both used as dopants, being co-injected with either toluene, acetonitrile or methanol solutions of the (thio)epoxides, with similar results. In both ESI and APCI, (thio)TMU is protonated preferentially, and these labile species dissociate promptly to yield (CH3)2N-C+=O and (CH3)2NCS+, which are the least acidic and most reactive (thio)acylium ions so far tested in the gas-phase Meerwein reaction. Under the low-energy ESI conditions set to favor both the formation of the (thio)acylium ion and ion/molecule reactions, (CH3)2NCO(S)+ react competitively with (thio)TMU to form acylated (thio)TMU and with the (thio)epoxide to form the characteristic Meerwein products. Enhanced selectivity in structural characterization or for the screening of (thio)epoxides is achieved by performing on-line collision-induced dissociation of Meerwein products, particularly for the more structurally complex (thio)epoxides.     

The thermal racemization of methyl-substituted hexahelicenes

Rates of racemization of several Me-substituted hexahelicenes have been measured. It appeared that Me groups at the positions 3, 4, 13 and 14 have no influence; at the positions 2 and 15 the effect is small; Me-substitution at C(1) and C(16) leads, however, to a large increase of the free energy of activation. From an analysis of the data the suggestion is made that the conformation of highest energy during racemisation of 1-methyl- and 1,16-dimethylhexahelicene (and possibly also of hepta and octahelicene) is that with the terminal rings in orthogonal position.     

Mechanism of thio acid/azide amidation

A combined experimental and computational mechanistic study of amide formation from thio acids and azides is described. The data support two distinct mechanistic pathways dependent on the electronic character of the azide component. Relatively electron-rich azides undergo bimolecular coupling with thiocarboxylates via an anion-accelerated [3+2] cycloaddition to give a thiatriazoline. Highly electron-poor azides couple via bimolecular union of the terminal nitrogen of the azide with sulfur of the thiocarboxylate to give a linear adduct. Cyclization of this intermediate gives a thiatriazoline. Decomposition to amide is found to proceed via retro-[3+2] cycloaddition of the neutral thiatriazoline intermediates. Computational analysis (DFT, 6-31+G(d)) identified pathways by which both classes of azide undergo [3+2] cycloaddition with thio acid to give thiatriazoline intermediates, although these paths are higher in energy than the thiocarboxylate amidations. These studies also establish that the reaction profile of electron-poor azides is attributable to a prior capture mechanism followed by intramolecular acylation.     

Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations

We present results of a theoretical analysis of the phosphorylation reaction in cAMP-dependent protein kinase using a combined quantum mechanical and molecular mechanics (QM/MM) approach. Detailed analysis of the reaction pathway is provided using a novel QM/MM implementation of the nudged elastic band method, finite temperature fluctuations of the protein environment are taken into account using free energy calculations, and an analysis of hydrogen bond interactions is performed on the basis of calculated frequency shifts. The late transfer of the substrate proton to the conserved aspartate (D166), the activation free energy of 15 kcal/mol, and the slight exothermic (-3 kcal/mol) character of the reaction are all consistent with the experimental data. The near attack conformation of D166 in the reactant state is maintained by interactions with threonine-201, asparagine-177, and most notably by a conserved water molecule serving as a strong structural link between the primary metal ion and the D166. The secondary Mg ion acts as a Lewis acid, attacking the beta-gamma bridging oxygen of ATP. This interaction, along with a strong hydrogen bond between the D166 and the substrate, contributes to the stabilization of the transition state. Lys-168 maintains a hydrogen bond to a transferring phosphoryl group throughout a reaction process. This interaction increases in the product state and contributes to its stabilization.     

Nucleophilic phosphine-catalyzed [3+2] cycloaddition of allenes with N-(thio)phosphoryl imines and acidic methanolysis of adducts N-(thio)phosphoryl 3-pyrrolines: a facile synthesis of free amine 3-pyrrolines

In this report, the dipolarophile imines with easily removable activating group O,O-diethyl(thio)phosphoryl have been investigated in the nucleophilic phosphine-catalyzed [3+2] cycloaddition reaction of electron-deficient allenes. Under the catalysis of a tertiary phosphine, N-(thio)phosphorylimines readily undergo the [3+2] cycloaddition reaction with ethyl 2,3-butadienoate or ethyl 2,3-pentadienoate, affording the corresponding N-(thio)phosphoryl 3-pyrrolines in moderate to high yields with good diastereoselectivity. Removal of the (thio)phosphoryl group from the adducts has been successfully achieved via the acidic methanolysis of the P-N bond, giving the free amine 3-pyrrolines in fair to good yields without severe aromatization. Thus, a facile synthesis of N-unsubstituted 3-pyrrolines is established from the phosphine-catalyzed [3+2] cycloaddition reaction of allenes with imines.     

Regio- and stereospecific synthesis of novel 3-enynyl-substituted thioflavones/flavones using a copper-free palladium-catalyzed reaction

[reaction: see text] A variety of 3-enynyl substituted flavones/thioflavones were synthesized via a sequential one-pot procedure using copper-free palladium-catalyzed cross coupling in a simple synthetic operation. The cross coupling between 3-iodo(thio)flavone and a broad range of terminal alkynes was carried out in the presence of Pd(PPh3)2Cl2 and triethylamine to afford the corresponding 3-enynyl derivatives in a regio- and stereoselective fashion. The best results are obtained by employing 3 equiv of the terminal alkynes. The process worked well irrespective of the substituents present on the (thio)flavone ring as well as in the terminal alkynes except arylalkynes. The reaction is quite regioselective, placing the substituent of the terminal alkyne at the far end of the double bond attached with the (thio)flavone ring. The orientation of the (thio)flavonyl and acetylenic moieties across the double bond was found to be syn in the products isolated. A tandem C-C bond-forming reaction in the presence of palladium catalyst rationalized the formation of coupled product. The catalytic process apparently involves heteroarylpalladium formation, regioselective addition to the C-C triple bond of the terminal alkyne, and subsequent displacement of palladium by another mole of alkyne. The present methodology is useful for the introduction of an enynyl moiety at the C-3 position of flavones and thioflavone rings to afford novel compounds of potential biological interest. In the presence of CuI the process afforded 3-alkynyl (thio)flavones in good yields.     

Chemistry of phosphorus ylides: Part 45 synthesis of phosphoranylidene,thietane, azetidine and thiazinane derivatives as potent chemo preventative agents

Reactions of nucleophilic active phosphacumulenes with iso(thio)cyanate compounds were performed. The reaction products depend on the nature of the reagent, substrate and the condition of the reaction used. New heterocyclic 4-membered or 6-membered sulfur and nitrogen compounds such as phosphoranylidene thietane, azetidine and thiazinane were obtained. On the other hand, the stable phosphonium ylides with the iso(thio)cyanate afforded phosphoranylidene thiocarbamoyl derivatives. Possible reaction mechanisms are considered and the structural assignments are based on compatible analytical and spectroscopic data.     

H2O3 as a reactive oxygen species: formation of 8-oxoguanine from its reaction with guanine

Reaction of guanine with H2O3 in the absence and presence of a water molecule leading to the formation of 8-oxoguanine (8-oxoG) was investigated. Initial calculations were performed using imidazole (Im) as a model for the five-membered ring of guanine. The reactant, intermediate, and product complexes as well as transition states were obtained in gas phase at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels of theory. In all the cases, except for the reactions involving imidazole, single-point energy calculations were performed in gas phase at the MP2/AUG-cc-pVDZ level of theory. Solvation calculations in aqueous media were carried out using the polarizable continuum model (PCM) of the self-consistent reaction field (SCRF) theory. Vibrational frequency analysis and intrinsic reaction coordinate (IRC) calculations were performed to ensure that the transition states connected the reactant and product complexes properly. Zero-point energy (ZPE)-corrected total energies and Gibbs free energies at 298.15 K in gas phase and aqueous media were obtained. When a reaction of H2O3 in place of H2O2 with guanine is considered, the major barrier energy which is encountered at the first step is almost halved showing that H2O3 would be much more reactive than H2O2. Considering the reaction schemes investigated here and the observed fact that H2O3 is dissociated easily under ambient conditions, it appears that H2O3 would serve as an effective reactive oxygen species.     

Preparation of thiochromans via thermal cyclization

Formation of the thiochroman ring system is achieved by a two step synthesis that involves heating 3‐thiophenyl‐1‐propanols or 4‐thiophenyl‐2‐butanols in toluene with catalytic amounts of p‐toluenesulfonic acid. The propanols are made by the addition of sulfur stabilized carbanions to styrene oxide, ethylene oxide, propylene oxide, and isobutylene oxide. The carbanions are generated by treatment of either benzyl phenyl sulfide or thioanisole with butyllithium. The effect of substitution at the 1 and 3 positions of the propanols on the reaction yields is discussed. The mechanism of the reaction apparently involves intramolecular electrophilic aromatic substitution rather than a Claisen or thio‐Claisen rearrangement.     

Activite optique de polyamines tertiaires du type poly[thio-(N-R1-N-R2 aminomethyl)-1 ethylene]

Ultra-violet, ORD and CD spectra of (?)poly[thio1-(N-N-diethylaminomethyl) ethylene] (Ia) prepared by stereoelective polymerization of racemic N-N-diethyl-N-(thiirane-2-ylmethyl) amine using ZnEt₂-(—) 3-3-dimethyl-1,2 butanediol as initiator system, of (+)poly[thio1-(N-N-diethyl aminomethyl) ethylene] obtained from a partially resolved enantiomer using ZnEt₂-CH₃OH as initiator system, of poly[thio1-(N-methyl-N-sec-butyl aminomethyl) ethylene] and of poly[thio1-(N-methyl-N-(1-phenylethyl) aminomethyl) ethylene] in organic solvents (tertiary amine form) and in water (hydrochloride form) are described. Observed Cotton effects are associated with electronic transitions of chromophores by comparison with model molecules: N-methyl2-aminobutane, ethyl-thio-2-methylbutane and polypropylene sulfide. For polyamine (Ia), their contributions to optical rotatory powers in the visible are evaluated after decomposition of corresponding CD curves in Gaussian partial Cotton effects. The effects of other optically active electronic transitions located below 180 nm are deduced by difference. Influence of positions of chromophores with regard to chiral centers and of the protonation of nitrogen atoms on observed Cotton effects are discussed.     

Reactivity of thio (amino) derivatives of the ω-(4-hydroxyaryl)alkyl type in radical reactions

The enthalpies, activation energies, and rate constants of the reactions of thio (amino) alkylphenols of different structures were calculated and compared with those of the reactions of alkyl-substituted phenols, alkoxyl and alkyl radicals, hydroperoxides, and nitrogen dioxide, as well as the reactions of phenoxyl radicals with molecules of the substrate being oxidized. The calculation was performed by the intersecting parabolas method using O-H bond energy data for phenols. The correlation between the molecular structure of the thio (amino) alkylphenols and their reactivity in radical reactions is considered.     

Mechanistic pathways of the hydroxyl radical reactions of quinoline. 2. Computational analysis of hydroxyl radical attack at C atoms

Density functional theory (DFT) calculations are employed to compare the mechanism of the *OH attacks at all carbon atoms in quinoline. The computational analysis of the energy surface for the reaction of *OH with quinoline reveals that the formation of OH adducts proceeds through exothermic formation of pi-complexes/H-bonded complexes. The gas-phase reactions have activation energies ranging from <1.3 kcal/mol for the attack at positions C3 through C8 to 8.6 kcal/mol for the attack at the C2 position. Solvation, as described by the CPCM cavity model, lowers these activation barriers so that the attack at all carbon atoms except C2 is effectively barrierless. The *OH attack at C2 in solution is significantly different than at all other quinoline positions because it involves the only transition structure with energy higher than that of the starting materials and with an energetic barrier of 5.1 kcal/mol. The specific solvation approach also corroborates this finding because the attack at C2 was shown to have an energy barrier of 2.3 kcal/mol compared to the barrierless attack at C5. These results are in agreement with our recent experimental studies but differ from literature reports on the degradation of quinoline using the photo-Fenton reaction.     

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution

Density-functional and semiempirical quantum methods and continuum dielectric and explicit solvation models are applied to study the role of solvation on the stabilization of native and thio-substituted transphosphorylation reactions. Extensive comparison is made between results obtained from the different methods. For the semiempirical methods, explicit solvation was treated using a hybrid quantum mechanical/molecular mechanical (QM/MM) approach and the implicit solvation was treated using a recently developed smooth solvation model implemented into a d-orbital semiempirical framework (MNDO/d-SCOSMO) within CHARMM. The different quantum and solvation methods were applied to the transesterification of a 3'-ribose,5'-methyl phosphodiester that serves as a nonenzymatic model for the self-cleavage reaction catalyzed by the hammerhead and hairpin ribozymes. Thio effects were studied for a double sulfur substitution at the nonbridging phosphoryl oxygen positions. The reaction profiles of both the native and double sulfur-substituted reactions from the MNDO/d-SCOSMO calculations were similar to the QM/MM results and consistent with the experimentally observed trends. These results underscore the need for a d-orbital semiempirical representation for phosphorus and sulfur for the study of experimentally observed thio effects in enzymatic and nonenzymatic phosphoryl transfer reactions. One of the major advantages of the present approach is that it can be applied to model chemical reactions at a significantly lower computational cost than either the density-functional calculations with implicit solvation or the semiempirical QM/MM simulations with explicit solvent.     

The intermediacy of metathiophosphonate PhPSO in the reaction of N-tert-butyl-P-phenylphosphonamidothioic acid with alcohols

Kinetic studies of the reaction of N-tert-butyl-P-phenylphosphonamidothioic acid (1) with alcohols were carried out in CH2Cl2 by means of 31P NMR spectrometry. The reaction is of the first order with respect to thio acid 1. The first-order rate constant at 30 degrees C increases with increasing methanol concentration below 0.25 M, but otherwise the rate constants are either independent of alcohol concentration (MeOH above 0.25 M, BuOH) or decrease with increasing alcohol concentration (i-PrOH, t-BuOH). The effect of alcohols on the order of the reaction and parameters of activation, as well as results of competition experiments, lead us to the conclusion that reaction of 1 with alcohols occurs by an elimination-addition mechanism involving the association of the thio acid 1 and the alcohol and then formation in the rate-determining step of an encounter complex 2' ' involving metathiophosphonate 4, amine, and alcohol. Metathiophosphonate 4 reacts preferentially with the alcohol as the encounter complex (primary alcohols) or after diffusion apart as a "free" intermediate (hindered alcohols).     

Ab initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations

We have developed a prediction method for the binding structures of ligands with proteins. Our method consists of three steps. First, replica-exchange umbrella sampling simulations are performed along the distance between a putative binding site of a protein and a ligand as the reaction coordinate. Second, we obtain the potential of mean force (PMF) of the unbiased system using the weighted histogram analysis method and determine the distance that corresponds to the global minimum of PMF. Third, structures that have this global-minimum distance and energy values around the average potential energy are collected and analyzed using the principal component analysis. We predict the binding structure as the global-minimum free energy state on the free energy landscapes along the two major principal component axes. As test cases, we applied our method to five protein-ligand complex systems. Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank.